This paper reports a study of the ship loading and discharging process at a container terminal. Our objective was to analyse the impact of different operational strategies on vessel handling times in order to derive managerial insights that can be used by terminal operators to manage this key performance indicator. As a basis for our study, a simulation model was implemented, validated, and verified to gain insight into the containers loading and discharging process. Four scenarios were constructed to resemble possible instances under which a vessel would operate at a Mexican container terminal, with the different operational strategies that were designed and evaluated for each scenario. An experimental framework was proposed, based on comparisons of scenarios and search experimentation, and employing a fractional factorial design to evaluate the impact of several factors on the vessel handling times. Our results emphasise that with an adequate design of the operation parameters, combined with the implementation of efficient stacking policies; it is possible to keep VHT under control. Conclusions and recommendations for further research are also discussed.